Multiple sequence alignment - TraesCS5D01G232600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G232600 chr5D 100.000 3344 0 0 1 3344 339711134 339714477 0.000000e+00 6176.0
1 TraesCS5D01G232600 chr5B 92.155 2664 103 41 203 2800 398707695 398710318 0.000000e+00 3664.0
2 TraesCS5D01G232600 chr5B 89.342 319 9 7 3027 3344 398712830 398713124 8.760000e-101 377.0
3 TraesCS5D01G232600 chr5A 91.338 2182 80 44 203 2339 440946455 440948572 0.000000e+00 2881.0
4 TraesCS5D01G232600 chr5A 87.556 450 23 17 2390 2831 440948584 440949008 1.080000e-134 490.0
5 TraesCS5D01G232600 chr5A 94.983 299 7 4 3051 3344 440949432 440949727 2.350000e-126 462.0
6 TraesCS5D01G232600 chr3A 89.706 204 21 0 1 204 688501711 688501914 9.200000e-66 261.0
7 TraesCS5D01G232600 chrUn 86.567 201 27 0 5 205 22824425 22824625 4.340000e-54 222.0
8 TraesCS5D01G232600 chr1A 87.958 191 17 5 16 203 584855837 584856024 1.560000e-53 220.0
9 TraesCS5D01G232600 chr3B 87.831 189 19 3 20 206 31874401 31874215 5.620000e-53 219.0
10 TraesCS5D01G232600 chr6A 86.869 198 19 6 16 209 606131951 606131757 7.270000e-52 215.0
11 TraesCS5D01G232600 chr7D 85.427 199 28 1 6 203 478571013 478571211 4.370000e-49 206.0
12 TraesCS5D01G232600 chr1B 85.930 199 21 6 16 209 333488839 333488643 4.370000e-49 206.0
13 TraesCS5D01G232600 chr2A 85.279 197 28 1 10 205 723886551 723886747 5.660000e-48 202.0
14 TraesCS5D01G232600 chr2A 75.871 402 74 18 1297 1691 58550332 58549947 2.050000e-42 183.0
15 TraesCS5D01G232600 chr6D 84.422 199 31 0 5 203 363062578 363062776 2.630000e-46 196.0
16 TraesCS5D01G232600 chr2D 75.123 406 77 19 1293 1691 59452529 59452141 5.740000e-38 169.0
17 TraesCS5D01G232600 chr1D 82.895 76 13 0 2902 2977 40794145 40794220 5.990000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G232600 chr5D 339711134 339714477 3343 False 6176.000000 6176 100.000000 1 3344 1 chr5D.!!$F1 3343
1 TraesCS5D01G232600 chr5B 398707695 398713124 5429 False 2020.500000 3664 90.748500 203 3344 2 chr5B.!!$F1 3141
2 TraesCS5D01G232600 chr5A 440946455 440949727 3272 False 1277.666667 2881 91.292333 203 3344 3 chr5A.!!$F1 3141

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
229 230 0.106318 AGGGATCATCAAAGGGCAGC 60.106 55.0 0.0 0.0 0.0 5.25 F
910 972 0.322726 GCCAACCCCGCCTAGTTAAA 60.323 55.0 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1629 1723 4.774503 AGGAAGCCGCAGAGCAGC 62.775 66.667 0.0 0.0 34.23 5.25 R
2874 5042 0.109458 GGCCGAAAATGAAACCGACC 60.109 55.000 0.0 0.0 0.00 4.79 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.113745 GGACCTTGCGATGCCATG 58.886 61.111 0.00 0.00 0.00 3.66
18 19 2.410469 GACCTTGCGATGCCATGC 59.590 61.111 0.00 0.00 0.00 4.06
19 20 3.129913 GACCTTGCGATGCCATGCC 62.130 63.158 0.00 0.00 0.00 4.40
20 21 3.142162 CCTTGCGATGCCATGCCA 61.142 61.111 0.00 0.00 0.00 4.92
21 22 2.712944 CCTTGCGATGCCATGCCAA 61.713 57.895 0.00 0.00 0.00 4.52
22 23 1.517694 CTTGCGATGCCATGCCAAC 60.518 57.895 0.00 0.00 0.00 3.77
23 24 2.215465 CTTGCGATGCCATGCCAACA 62.215 55.000 0.00 0.00 0.00 3.33
24 25 2.202650 GCGATGCCATGCCAACAC 60.203 61.111 0.00 0.00 0.00 3.32
25 26 2.703798 GCGATGCCATGCCAACACT 61.704 57.895 0.00 0.00 0.00 3.55
26 27 1.885157 CGATGCCATGCCAACACTT 59.115 52.632 0.00 0.00 0.00 3.16
27 28 1.093972 CGATGCCATGCCAACACTTA 58.906 50.000 0.00 0.00 0.00 2.24
28 29 1.202177 CGATGCCATGCCAACACTTAC 60.202 52.381 0.00 0.00 0.00 2.34
29 30 1.818060 GATGCCATGCCAACACTTACA 59.182 47.619 0.00 0.00 0.00 2.41
30 31 1.921982 TGCCATGCCAACACTTACAT 58.078 45.000 0.00 0.00 0.00 2.29
31 32 1.545136 TGCCATGCCAACACTTACATG 59.455 47.619 0.00 0.00 39.65 3.21
32 33 1.736696 GCCATGCCAACACTTACATGC 60.737 52.381 0.00 0.00 38.83 4.06
33 34 1.467883 CCATGCCAACACTTACATGCG 60.468 52.381 0.00 0.00 38.83 4.73
34 35 0.810648 ATGCCAACACTTACATGCGG 59.189 50.000 0.00 0.00 0.00 5.69
35 36 1.240641 TGCCAACACTTACATGCGGG 61.241 55.000 0.00 0.00 0.00 6.13
36 37 1.506262 CCAACACTTACATGCGGGC 59.494 57.895 0.00 0.00 0.00 6.13
37 38 1.506262 CAACACTTACATGCGGGCC 59.494 57.895 0.00 0.00 0.00 5.80
38 39 1.074072 AACACTTACATGCGGGCCA 59.926 52.632 4.39 0.00 0.00 5.36
39 40 0.960364 AACACTTACATGCGGGCCAG 60.960 55.000 4.39 0.00 0.00 4.85
40 41 2.114670 CACTTACATGCGGGCCAGG 61.115 63.158 4.39 0.00 0.00 4.45
41 42 3.211963 CTTACATGCGGGCCAGGC 61.212 66.667 4.39 1.26 0.00 4.85
51 52 4.567318 GGCCAGGCCTGTCATAAG 57.433 61.111 30.63 15.52 46.69 1.73
52 53 1.825622 GGCCAGGCCTGTCATAAGC 60.826 63.158 30.63 23.83 46.69 3.09
53 54 2.182842 GCCAGGCCTGTCATAAGCG 61.183 63.158 30.63 14.04 0.00 4.68
54 55 2.182842 CCAGGCCTGTCATAAGCGC 61.183 63.158 30.63 0.00 0.00 5.92
55 56 2.202932 AGGCCTGTCATAAGCGCG 60.203 61.111 3.11 0.00 0.00 6.86
56 57 2.511600 GGCCTGTCATAAGCGCGT 60.512 61.111 8.43 0.00 0.00 6.01
57 58 2.106683 GGCCTGTCATAAGCGCGTT 61.107 57.895 8.43 0.00 0.00 4.84
58 59 1.644786 GGCCTGTCATAAGCGCGTTT 61.645 55.000 13.97 13.97 0.00 3.60
59 60 1.003851 GCCTGTCATAAGCGCGTTTA 58.996 50.000 17.79 17.79 0.00 2.01
60 61 1.395608 GCCTGTCATAAGCGCGTTTAA 59.604 47.619 19.29 1.05 0.00 1.52
61 62 2.159626 GCCTGTCATAAGCGCGTTTAAA 60.160 45.455 19.29 8.14 0.00 1.52
62 63 3.668491 GCCTGTCATAAGCGCGTTTAAAA 60.668 43.478 19.29 7.79 0.00 1.52
63 64 4.658071 CCTGTCATAAGCGCGTTTAAAAT 58.342 39.130 19.29 1.37 0.00 1.82
64 65 4.495472 CCTGTCATAAGCGCGTTTAAAATG 59.505 41.667 19.29 14.03 0.00 2.32
65 66 5.284428 TGTCATAAGCGCGTTTAAAATGA 57.716 34.783 19.29 16.02 0.00 2.57
66 67 5.690816 TGTCATAAGCGCGTTTAAAATGAA 58.309 33.333 19.29 8.13 0.00 2.57
67 68 5.566016 TGTCATAAGCGCGTTTAAAATGAAC 59.434 36.000 19.29 13.35 0.00 3.18
91 92 6.633668 GAATCGGTCGATTTATAGACATGG 57.366 41.667 17.90 0.00 43.98 3.66
92 93 5.723672 ATCGGTCGATTTATAGACATGGT 57.276 39.130 0.00 0.00 39.01 3.55
93 94 6.829229 ATCGGTCGATTTATAGACATGGTA 57.171 37.500 0.00 0.00 39.01 3.25
94 95 6.250344 TCGGTCGATTTATAGACATGGTAG 57.750 41.667 0.00 0.00 39.01 3.18
95 96 5.766670 TCGGTCGATTTATAGACATGGTAGT 59.233 40.000 0.00 0.00 39.01 2.73
96 97 6.263842 TCGGTCGATTTATAGACATGGTAGTT 59.736 38.462 0.00 0.00 39.01 2.24
97 98 6.921857 CGGTCGATTTATAGACATGGTAGTTT 59.078 38.462 0.00 0.00 39.01 2.66
98 99 7.437267 CGGTCGATTTATAGACATGGTAGTTTT 59.563 37.037 0.00 0.00 39.01 2.43
99 100 9.106070 GGTCGATTTATAGACATGGTAGTTTTT 57.894 33.333 0.00 0.00 39.01 1.94
108 109 9.816787 ATAGACATGGTAGTTTTTAGGGAAAAA 57.183 29.630 0.00 0.00 41.24 1.94
109 110 8.721133 AGACATGGTAGTTTTTAGGGAAAAAT 57.279 30.769 0.00 0.00 44.29 1.82
110 111 9.154632 AGACATGGTAGTTTTTAGGGAAAAATT 57.845 29.630 0.00 0.00 44.29 1.82
134 135 5.874895 ATAAGAAAGTGGTAGTTTTCGGC 57.125 39.130 0.00 0.00 38.13 5.54
135 136 3.202829 AGAAAGTGGTAGTTTTCGGCA 57.797 42.857 0.00 0.00 38.13 5.69
136 137 3.751518 AGAAAGTGGTAGTTTTCGGCAT 58.248 40.909 0.00 0.00 38.13 4.40
137 138 4.901868 AGAAAGTGGTAGTTTTCGGCATA 58.098 39.130 0.00 0.00 38.13 3.14
138 139 5.310451 AGAAAGTGGTAGTTTTCGGCATAA 58.690 37.500 0.00 0.00 38.13 1.90
139 140 5.766174 AGAAAGTGGTAGTTTTCGGCATAAA 59.234 36.000 0.00 0.00 38.13 1.40
140 141 6.433093 AGAAAGTGGTAGTTTTCGGCATAAAT 59.567 34.615 0.00 0.00 38.13 1.40
141 142 6.584185 AAGTGGTAGTTTTCGGCATAAATT 57.416 33.333 0.00 0.00 0.00 1.82
142 143 6.584185 AGTGGTAGTTTTCGGCATAAATTT 57.416 33.333 0.00 0.00 0.00 1.82
143 144 6.386654 AGTGGTAGTTTTCGGCATAAATTTG 58.613 36.000 0.00 0.00 0.00 2.32
144 145 6.015772 AGTGGTAGTTTTCGGCATAAATTTGT 60.016 34.615 0.00 0.00 0.00 2.83
145 146 7.175293 AGTGGTAGTTTTCGGCATAAATTTGTA 59.825 33.333 0.00 0.00 0.00 2.41
146 147 7.808856 GTGGTAGTTTTCGGCATAAATTTGTAA 59.191 33.333 0.00 0.00 0.00 2.41
147 148 8.358148 TGGTAGTTTTCGGCATAAATTTGTAAA 58.642 29.630 0.00 0.00 0.00 2.01
148 149 8.856247 GGTAGTTTTCGGCATAAATTTGTAAAG 58.144 33.333 0.00 0.00 0.00 1.85
149 150 9.401873 GTAGTTTTCGGCATAAATTTGTAAAGT 57.598 29.630 0.00 0.00 0.00 2.66
150 151 8.293114 AGTTTTCGGCATAAATTTGTAAAGTG 57.707 30.769 0.00 0.00 0.00 3.16
151 152 7.383843 AGTTTTCGGCATAAATTTGTAAAGTGG 59.616 33.333 0.00 0.00 0.00 4.00
152 153 5.968528 TCGGCATAAATTTGTAAAGTGGT 57.031 34.783 0.00 0.00 0.00 4.16
153 154 7.450124 TTCGGCATAAATTTGTAAAGTGGTA 57.550 32.000 0.00 0.00 0.00 3.25
154 155 7.079182 TCGGCATAAATTTGTAAAGTGGTAG 57.921 36.000 0.00 0.00 0.00 3.18
155 156 6.655848 TCGGCATAAATTTGTAAAGTGGTAGT 59.344 34.615 0.00 0.00 0.00 2.73
156 157 7.175293 TCGGCATAAATTTGTAAAGTGGTAGTT 59.825 33.333 0.00 0.00 0.00 2.24
157 158 7.810759 CGGCATAAATTTGTAAAGTGGTAGTTT 59.189 33.333 0.00 0.00 0.00 2.66
158 159 8.921670 GGCATAAATTTGTAAAGTGGTAGTTTG 58.078 33.333 0.00 0.00 0.00 2.93
159 160 9.471084 GCATAAATTTGTAAAGTGGTAGTTTGT 57.529 29.630 0.00 0.00 0.00 2.83
163 164 6.622833 TTTGTAAAGTGGTAGTTTGTAGGC 57.377 37.500 0.00 0.00 0.00 3.93
164 165 5.293319 TGTAAAGTGGTAGTTTGTAGGCA 57.707 39.130 0.00 0.00 0.00 4.75
165 166 5.058490 TGTAAAGTGGTAGTTTGTAGGCAC 58.942 41.667 0.00 0.00 0.00 5.01
166 167 2.450609 AGTGGTAGTTTGTAGGCACG 57.549 50.000 0.00 0.00 0.00 5.34
167 168 1.001633 AGTGGTAGTTTGTAGGCACGG 59.998 52.381 0.00 0.00 0.00 4.94
168 169 1.050204 TGGTAGTTTGTAGGCACGGT 58.950 50.000 0.00 0.00 0.00 4.83
169 170 1.417145 TGGTAGTTTGTAGGCACGGTT 59.583 47.619 0.00 0.00 0.00 4.44
170 171 2.158784 TGGTAGTTTGTAGGCACGGTTT 60.159 45.455 0.00 0.00 0.00 3.27
171 172 3.070734 TGGTAGTTTGTAGGCACGGTTTA 59.929 43.478 0.00 0.00 0.00 2.01
172 173 4.064388 GGTAGTTTGTAGGCACGGTTTAA 58.936 43.478 0.00 0.00 0.00 1.52
173 174 4.083855 GGTAGTTTGTAGGCACGGTTTAAC 60.084 45.833 0.00 0.00 0.00 2.01
174 175 3.543665 AGTTTGTAGGCACGGTTTAACA 58.456 40.909 0.00 0.00 0.00 2.41
175 176 3.946558 AGTTTGTAGGCACGGTTTAACAA 59.053 39.130 0.00 0.00 0.00 2.83
176 177 4.398673 AGTTTGTAGGCACGGTTTAACAAA 59.601 37.500 0.00 0.00 35.21 2.83
177 178 5.068067 AGTTTGTAGGCACGGTTTAACAAAT 59.932 36.000 9.72 0.49 38.60 2.32
178 179 4.491234 TGTAGGCACGGTTTAACAAATG 57.509 40.909 0.00 0.00 0.00 2.32
179 180 3.253677 TGTAGGCACGGTTTAACAAATGG 59.746 43.478 0.00 0.00 0.00 3.16
180 181 2.312390 AGGCACGGTTTAACAAATGGT 58.688 42.857 0.00 0.00 0.00 3.55
181 182 2.035321 AGGCACGGTTTAACAAATGGTG 59.965 45.455 0.00 0.00 32.79 4.17
182 183 2.399448 GCACGGTTTAACAAATGGTGG 58.601 47.619 0.00 0.00 31.32 4.61
183 184 2.223852 GCACGGTTTAACAAATGGTGGT 60.224 45.455 0.00 0.00 31.32 4.16
184 185 3.004524 GCACGGTTTAACAAATGGTGGTA 59.995 43.478 0.00 0.00 31.32 3.25
185 186 4.789784 CACGGTTTAACAAATGGTGGTAG 58.210 43.478 0.00 0.00 28.77 3.18
186 187 4.276431 CACGGTTTAACAAATGGTGGTAGT 59.724 41.667 0.00 0.00 28.77 2.73
187 188 4.888823 ACGGTTTAACAAATGGTGGTAGTT 59.111 37.500 0.00 0.00 28.77 2.24
188 189 5.360429 ACGGTTTAACAAATGGTGGTAGTTT 59.640 36.000 0.00 0.00 28.77 2.66
189 190 6.127394 ACGGTTTAACAAATGGTGGTAGTTTT 60.127 34.615 0.00 0.00 28.77 2.43
190 191 6.757478 CGGTTTAACAAATGGTGGTAGTTTTT 59.243 34.615 0.00 0.00 28.77 1.94
229 230 0.106318 AGGGATCATCAAAGGGCAGC 60.106 55.000 0.00 0.00 0.00 5.25
235 236 2.300967 ATCAAAGGGCAGCGAGGGA 61.301 57.895 0.00 0.00 0.00 4.20
248 249 1.900545 CGAGGGAAGGAGGGTCAACC 61.901 65.000 0.00 0.00 40.67 3.77
271 272 5.448632 CCGTGGTCTAAATAGAATTGGCAAC 60.449 44.000 0.00 0.00 33.47 4.17
279 280 8.020819 TCTAAATAGAATTGGCAACGAAAACAG 58.979 33.333 0.00 0.00 42.51 3.16
323 334 5.899631 AGGAAAACAGTGGTTAAGAGGTA 57.100 39.130 0.00 0.00 35.82 3.08
331 342 1.203052 TGGTTAAGAGGTACGCGAAGG 59.797 52.381 15.93 0.00 0.00 3.46
335 346 0.526662 AAGAGGTACGCGAAGGTGAG 59.473 55.000 15.93 0.00 0.00 3.51
548 587 2.799371 CGTCACCGGGCTACTCTC 59.201 66.667 6.32 0.00 0.00 3.20
549 588 2.772691 CGTCACCGGGCTACTCTCC 61.773 68.421 6.32 0.00 0.00 3.71
550 589 1.380112 GTCACCGGGCTACTCTCCT 60.380 63.158 6.32 0.00 0.00 3.69
551 590 1.076923 TCACCGGGCTACTCTCCTC 60.077 63.158 6.32 0.00 0.00 3.71
552 591 1.076632 CACCGGGCTACTCTCCTCT 60.077 63.158 6.32 0.00 0.00 3.69
608 647 3.199442 TCACATTTGTCCCCTCTCCTA 57.801 47.619 0.00 0.00 0.00 2.94
671 710 4.778143 CACACGCCCCCTAGCCAC 62.778 72.222 0.00 0.00 0.00 5.01
678 717 2.040884 CCCCTAGCCACCTAGCCA 60.041 66.667 0.00 0.00 39.81 4.75
679 718 2.444256 CCCCTAGCCACCTAGCCAC 61.444 68.421 0.00 0.00 39.81 5.01
680 719 2.444256 CCCTAGCCACCTAGCCACC 61.444 68.421 0.00 0.00 39.81 4.61
681 720 1.383248 CCTAGCCACCTAGCCACCT 60.383 63.158 0.00 0.00 39.81 4.00
910 972 0.322726 GCCAACCCCGCCTAGTTAAA 60.323 55.000 0.00 0.00 0.00 1.52
911 973 1.746470 CCAACCCCGCCTAGTTAAAG 58.254 55.000 0.00 0.00 0.00 1.85
918 980 2.372172 CCCGCCTAGTTAAAGATCCCAT 59.628 50.000 0.00 0.00 0.00 4.00
969 1043 6.417930 GTGATTAGTGAACTTCCAAAACAAGC 59.582 38.462 0.00 0.00 0.00 4.01
970 1044 5.906113 TTAGTGAACTTCCAAAACAAGCA 57.094 34.783 0.00 0.00 0.00 3.91
972 1046 5.343307 AGTGAACTTCCAAAACAAGCAAT 57.657 34.783 0.00 0.00 0.00 3.56
974 1048 4.507756 GTGAACTTCCAAAACAAGCAATCC 59.492 41.667 0.00 0.00 0.00 3.01
975 1049 4.405358 TGAACTTCCAAAACAAGCAATCCT 59.595 37.500 0.00 0.00 0.00 3.24
979 1053 2.293122 TCCAAAACAAGCAATCCTCGTG 59.707 45.455 0.00 0.00 0.00 4.35
980 1054 2.607771 CCAAAACAAGCAATCCTCGTGG 60.608 50.000 0.00 0.00 0.00 4.94
981 1055 0.598065 AAACAAGCAATCCTCGTGGC 59.402 50.000 0.00 0.00 0.00 5.01
982 1056 0.537143 AACAAGCAATCCTCGTGGCA 60.537 50.000 0.00 0.00 0.00 4.92
983 1057 0.957395 ACAAGCAATCCTCGTGGCAG 60.957 55.000 0.00 0.00 0.00 4.85
984 1058 2.042831 AAGCAATCCTCGTGGCAGC 61.043 57.895 0.00 2.79 0.00 5.25
985 1059 3.512516 GCAATCCTCGTGGCAGCC 61.513 66.667 3.66 3.66 0.00 4.85
986 1060 2.046023 CAATCCTCGTGGCAGCCA 60.046 61.111 11.22 11.22 0.00 4.75
987 1061 2.110967 CAATCCTCGTGGCAGCCAG 61.111 63.158 16.83 9.54 32.34 4.85
988 1062 2.293318 AATCCTCGTGGCAGCCAGA 61.293 57.895 16.83 13.55 32.34 3.86
989 1063 2.249413 AATCCTCGTGGCAGCCAGAG 62.249 60.000 16.83 21.62 32.34 3.35
1154 1248 1.488705 AAGGTCATCGACAAGGCCCA 61.489 55.000 0.00 0.00 33.68 5.36
1819 1913 2.954753 CTCACGCCGTGGTTCAAGC 61.955 63.158 18.32 0.00 33.87 4.01
2357 2451 1.513158 CGTGATCTCAGGCCGTTCT 59.487 57.895 0.00 0.00 0.00 3.01
2404 2498 5.128663 ACAAATGGGGCAAATTAGTGATACC 59.871 40.000 0.00 0.00 0.00 2.73
2478 2572 2.235650 ACTAGTAAGTTTCTTCGGGGCC 59.764 50.000 0.00 0.00 29.00 5.80
2494 2592 1.676678 GGCCGCCATGACTAGAGTGA 61.677 60.000 3.91 0.00 0.00 3.41
2550 2650 4.156922 AGAGAGGTGTTTGTAGATGACGAG 59.843 45.833 0.00 0.00 0.00 4.18
2652 2760 2.559440 GCTTCTGCTCCTTGTGATAGG 58.441 52.381 0.00 0.00 36.59 2.57
2653 2761 2.169352 GCTTCTGCTCCTTGTGATAGGA 59.831 50.000 0.00 0.00 42.02 2.94
2654 2762 3.369892 GCTTCTGCTCCTTGTGATAGGAA 60.370 47.826 0.00 0.00 43.57 3.36
2655 2763 4.440880 CTTCTGCTCCTTGTGATAGGAAG 58.559 47.826 0.00 0.00 43.57 3.46
2656 2764 2.768527 TCTGCTCCTTGTGATAGGAAGG 59.231 50.000 0.00 0.00 43.57 3.46
2721 2841 7.984050 AGATTCTTATCAGTTGATGTGACGAAT 59.016 33.333 4.90 5.71 36.05 3.34
2722 2842 7.905604 TTCTTATCAGTTGATGTGACGAATT 57.094 32.000 4.90 0.00 36.05 2.17
2744 2864 2.758423 TGAACTGCTAGGAATCGTGCTA 59.242 45.455 0.00 0.00 0.00 3.49
2815 4983 3.873952 GAGCTTACCTCAGCCATTTGTAG 59.126 47.826 0.00 0.00 41.12 2.74
2832 5000 7.393234 CCATTTGTAGGTGTCAAAAGGATTAGA 59.607 37.037 6.77 0.00 42.52 2.10
2834 5002 5.801380 TGTAGGTGTCAAAAGGATTAGACC 58.199 41.667 0.00 0.00 33.79 3.85
2835 5003 4.302559 AGGTGTCAAAAGGATTAGACCC 57.697 45.455 0.00 0.00 33.79 4.46
2837 5005 4.010349 GGTGTCAAAAGGATTAGACCCTG 58.990 47.826 0.00 0.00 33.79 4.45
2838 5006 4.506802 GGTGTCAAAAGGATTAGACCCTGT 60.507 45.833 0.00 0.00 33.79 4.00
2839 5007 5.070685 GTGTCAAAAGGATTAGACCCTGTT 58.929 41.667 0.00 0.00 33.79 3.16
2841 5009 5.534654 TGTCAAAAGGATTAGACCCTGTTTG 59.465 40.000 0.00 0.00 33.79 2.93
2842 5010 5.048013 GTCAAAAGGATTAGACCCTGTTTGG 60.048 44.000 0.20 0.00 35.27 3.28
2853 5021 2.227194 CCCTGTTTGGTCTAACACACC 58.773 52.381 0.00 0.00 34.50 4.16
2855 5023 2.878406 CCTGTTTGGTCTAACACACCTG 59.122 50.000 0.00 0.00 34.50 4.00
2857 5025 3.945285 CTGTTTGGTCTAACACACCTGTT 59.055 43.478 0.00 0.00 43.39 3.16
2858 5026 5.100344 TGTTTGGTCTAACACACCTGTTA 57.900 39.130 0.00 0.00 41.15 2.41
2859 5027 5.498393 TGTTTGGTCTAACACACCTGTTAA 58.502 37.500 0.00 0.00 41.40 2.01
2860 5028 6.123651 TGTTTGGTCTAACACACCTGTTAAT 58.876 36.000 0.00 0.00 41.40 1.40
2862 5030 7.940137 TGTTTGGTCTAACACACCTGTTAATAT 59.060 33.333 0.00 0.00 41.40 1.28
2863 5031 9.439500 GTTTGGTCTAACACACCTGTTAATATA 57.561 33.333 0.00 0.00 41.40 0.86
2864 5032 9.439500 TTTGGTCTAACACACCTGTTAATATAC 57.561 33.333 0.00 0.00 41.40 1.47
2865 5033 7.259882 TGGTCTAACACACCTGTTAATATACG 58.740 38.462 0.00 0.00 41.40 3.06
2867 5035 6.199719 GTCTAACACACCTGTTAATATACGCC 59.800 42.308 0.00 0.00 41.40 5.68
2869 5037 4.690122 ACACACCTGTTAATATACGCCTC 58.310 43.478 0.00 0.00 0.00 4.70
2870 5038 4.404715 ACACACCTGTTAATATACGCCTCT 59.595 41.667 0.00 0.00 0.00 3.69
2871 5039 4.745125 CACACCTGTTAATATACGCCTCTG 59.255 45.833 0.00 0.00 0.00 3.35
2872 5040 3.741344 CACCTGTTAATATACGCCTCTGC 59.259 47.826 0.00 0.00 0.00 4.26
2873 5041 3.386726 ACCTGTTAATATACGCCTCTGCA 59.613 43.478 0.00 0.00 37.32 4.41
2874 5042 3.990469 CCTGTTAATATACGCCTCTGCAG 59.010 47.826 7.63 7.63 37.32 4.41
2875 5043 3.990092 TGTTAATATACGCCTCTGCAGG 58.010 45.455 15.13 0.00 43.82 4.85
2879 5047 1.452953 TATACGCCTCTGCAGGTCGG 61.453 60.000 15.13 13.06 42.74 4.79
2881 5049 4.379243 CGCCTCTGCAGGTCGGTT 62.379 66.667 15.13 0.00 42.74 4.44
2882 5050 2.032681 GCCTCTGCAGGTCGGTTT 59.967 61.111 15.13 0.00 42.74 3.27
2885 5053 0.036010 CCTCTGCAGGTCGGTTTCAT 60.036 55.000 15.13 0.00 34.60 2.57
2886 5054 1.611673 CCTCTGCAGGTCGGTTTCATT 60.612 52.381 15.13 0.00 34.60 2.57
2889 5057 2.552315 TCTGCAGGTCGGTTTCATTTTC 59.448 45.455 15.13 0.00 0.00 2.29
2891 5059 1.401018 GCAGGTCGGTTTCATTTTCGG 60.401 52.381 0.00 0.00 0.00 4.30
2893 5061 0.109458 GGTCGGTTTCATTTTCGGCC 60.109 55.000 0.00 0.00 40.19 6.13
2894 5062 0.109458 GTCGGTTTCATTTTCGGCCC 60.109 55.000 0.00 0.00 0.00 5.80
2895 5063 1.154112 CGGTTTCATTTTCGGCCCG 60.154 57.895 0.00 0.00 0.00 6.13
2896 5064 1.579084 CGGTTTCATTTTCGGCCCGA 61.579 55.000 0.00 0.00 36.12 5.14
2904 5072 4.609995 TTCGGCCCGAAATCACTC 57.390 55.556 17.74 0.00 43.00 3.51
2906 5074 0.251916 TTCGGCCCGAAATCACTCAT 59.748 50.000 17.74 0.00 43.00 2.90
2907 5075 0.461870 TCGGCCCGAAATCACTCATG 60.462 55.000 1.70 0.00 31.06 3.07
2909 5077 1.728490 GGCCCGAAATCACTCATGCC 61.728 60.000 0.00 0.00 0.00 4.40
2910 5078 1.728490 GCCCGAAATCACTCATGCCC 61.728 60.000 0.00 0.00 0.00 5.36
2912 5080 1.019673 CCGAAATCACTCATGCCCAG 58.980 55.000 0.00 0.00 0.00 4.45
2915 5083 3.270027 CGAAATCACTCATGCCCAGTAA 58.730 45.455 0.00 0.00 0.00 2.24
2916 5084 3.310774 CGAAATCACTCATGCCCAGTAAG 59.689 47.826 0.00 0.00 0.00 2.34
2917 5085 4.517285 GAAATCACTCATGCCCAGTAAGA 58.483 43.478 0.00 0.00 0.00 2.10
2918 5086 4.785346 AATCACTCATGCCCAGTAAGAT 57.215 40.909 0.00 0.00 0.00 2.40
2919 5087 5.894298 AATCACTCATGCCCAGTAAGATA 57.106 39.130 0.00 0.00 0.00 1.98
2920 5088 4.672587 TCACTCATGCCCAGTAAGATAC 57.327 45.455 0.00 0.00 0.00 2.24
2925 5093 4.769688 TCATGCCCAGTAAGATACACTTG 58.230 43.478 0.00 0.00 39.38 3.16
2926 5094 4.225042 TCATGCCCAGTAAGATACACTTGT 59.775 41.667 0.00 0.00 39.38 3.16
2928 5096 5.748670 TGCCCAGTAAGATACACTTGTAA 57.251 39.130 0.00 0.00 39.38 2.41
2932 5100 7.668052 TGCCCAGTAAGATACACTTGTAAATTT 59.332 33.333 0.00 0.00 39.38 1.82
2962 5130 9.651913 ACCATTGTGTTAAATTACATCAAATCC 57.348 29.630 0.00 0.00 0.00 3.01
2963 5131 9.650539 CCATTGTGTTAAATTACATCAAATCCA 57.349 29.630 0.00 0.00 0.00 3.41
2966 5134 8.755696 TGTGTTAAATTACATCAAATCCAAGC 57.244 30.769 0.00 0.00 0.00 4.01
2967 5135 7.540400 TGTGTTAAATTACATCAAATCCAAGCG 59.460 33.333 0.00 0.00 0.00 4.68
2968 5136 7.540745 GTGTTAAATTACATCAAATCCAAGCGT 59.459 33.333 0.00 0.00 0.00 5.07
2969 5137 7.540400 TGTTAAATTACATCAAATCCAAGCGTG 59.460 33.333 0.00 0.00 0.00 5.34
2972 5140 0.179129 CATCAAATCCAAGCGTGGCC 60.179 55.000 14.54 0.00 45.54 5.36
2975 5143 1.173043 CAAATCCAAGCGTGGCCTTA 58.827 50.000 14.54 0.00 45.54 2.69
2976 5144 1.133025 CAAATCCAAGCGTGGCCTTAG 59.867 52.381 14.54 0.00 45.54 2.18
2978 5146 1.271840 ATCCAAGCGTGGCCTTAGGA 61.272 55.000 14.54 3.23 45.54 2.94
2979 5147 1.002624 CCAAGCGTGGCCTTAGGAA 60.003 57.895 5.51 0.00 38.35 3.36
2981 5149 0.734889 CAAGCGTGGCCTTAGGAATG 59.265 55.000 3.32 0.00 0.00 2.67
2982 5150 0.618458 AAGCGTGGCCTTAGGAATGA 59.382 50.000 3.32 0.00 0.00 2.57
2983 5151 0.179000 AGCGTGGCCTTAGGAATGAG 59.821 55.000 3.32 0.00 0.00 2.90
2985 5153 1.138266 GCGTGGCCTTAGGAATGAGTA 59.862 52.381 3.32 0.00 0.00 2.59
2986 5154 2.803492 GCGTGGCCTTAGGAATGAGTAG 60.803 54.545 3.32 0.00 0.00 2.57
2987 5155 2.693591 CGTGGCCTTAGGAATGAGTAGA 59.306 50.000 3.32 0.00 0.00 2.59
2989 5157 4.698575 GTGGCCTTAGGAATGAGTAGAAG 58.301 47.826 3.32 0.00 0.00 2.85
2990 5158 3.134804 TGGCCTTAGGAATGAGTAGAAGC 59.865 47.826 3.32 0.00 0.00 3.86
2991 5159 3.389656 GGCCTTAGGAATGAGTAGAAGCT 59.610 47.826 0.69 0.00 0.00 3.74
2994 5162 5.738783 GCCTTAGGAATGAGTAGAAGCTGAG 60.739 48.000 0.69 0.00 0.00 3.35
2995 5163 5.362430 CCTTAGGAATGAGTAGAAGCTGAGT 59.638 44.000 0.00 0.00 0.00 3.41
2997 5165 5.845391 AGGAATGAGTAGAAGCTGAGTAC 57.155 43.478 0.00 0.00 0.00 2.73
2998 5166 4.647399 AGGAATGAGTAGAAGCTGAGTACC 59.353 45.833 0.00 0.00 0.00 3.34
2999 5167 4.647399 GGAATGAGTAGAAGCTGAGTACCT 59.353 45.833 0.00 0.00 0.00 3.08
3012 5209 5.100943 GCTGAGTACCTTTACGAAGTTAGG 58.899 45.833 0.00 0.00 37.78 2.69
3014 5211 6.571150 GCTGAGTACCTTTACGAAGTTAGGAA 60.571 42.308 0.00 0.00 37.78 3.36
3015 5212 6.681777 TGAGTACCTTTACGAAGTTAGGAAC 58.318 40.000 0.00 0.00 37.78 3.62
3017 5214 6.450545 AGTACCTTTACGAAGTTAGGAACAC 58.549 40.000 0.00 0.00 37.78 3.32
3019 5216 3.676646 CCTTTACGAAGTTAGGAACACCG 59.323 47.826 0.00 0.00 37.78 4.94
3038 5465 5.305386 ACACCGTAGACTTTAAAACCCTAGT 59.695 40.000 0.00 0.00 0.00 2.57
3039 5466 6.493458 ACACCGTAGACTTTAAAACCCTAGTA 59.507 38.462 0.00 0.00 0.00 1.82
3040 5467 7.031975 CACCGTAGACTTTAAAACCCTAGTAG 58.968 42.308 0.00 0.00 0.00 2.57
3041 5468 6.721668 ACCGTAGACTTTAAAACCCTAGTAGT 59.278 38.462 0.00 0.00 0.00 2.73
3059 5486 9.886132 CCTAGTAGTTTTTACATGTAGAACCAT 57.114 33.333 21.22 14.10 0.00 3.55
3111 5538 7.255416 GCCAATCCTTCTGGAATAGATTTCTTC 60.255 40.741 0.00 0.00 46.80 2.87
3183 5615 7.044798 CCCAACAAACCATGACTAAAAGAAAA 58.955 34.615 0.00 0.00 0.00 2.29
3204 5636 2.902846 CCAACAAACACGGGCGGA 60.903 61.111 0.00 0.00 0.00 5.54
3205 5637 2.482333 CCAACAAACACGGGCGGAA 61.482 57.895 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.113745 CATGGCATCGCAAGGTCC 58.886 61.111 0.00 0.00 38.47 4.46
1 2 2.410469 GCATGGCATCGCAAGGTC 59.590 61.111 14.33 0.00 38.47 3.85
2 3 3.142838 GGCATGGCATCGCAAGGT 61.143 61.111 15.47 0.00 38.47 3.50
3 4 2.712944 TTGGCATGGCATCGCAAGG 61.713 57.895 23.96 0.90 38.47 3.61
4 5 1.517694 GTTGGCATGGCATCGCAAG 60.518 57.895 23.96 1.55 0.00 4.01
5 6 2.273912 TGTTGGCATGGCATCGCAA 61.274 52.632 23.96 4.41 0.00 4.85
6 7 2.675772 TGTTGGCATGGCATCGCA 60.676 55.556 23.96 18.32 0.00 5.10
7 8 2.202650 GTGTTGGCATGGCATCGC 60.203 61.111 23.96 23.39 0.00 4.58
8 9 1.093972 TAAGTGTTGGCATGGCATCG 58.906 50.000 23.96 0.00 0.00 3.84
9 10 1.818060 TGTAAGTGTTGGCATGGCATC 59.182 47.619 23.96 21.91 0.00 3.91
10 11 1.921982 TGTAAGTGTTGGCATGGCAT 58.078 45.000 23.96 10.24 0.00 4.40
11 12 1.545136 CATGTAAGTGTTGGCATGGCA 59.455 47.619 19.43 19.43 36.15 4.92
12 13 1.736696 GCATGTAAGTGTTGGCATGGC 60.737 52.381 13.29 13.29 39.11 4.40
13 14 1.467883 CGCATGTAAGTGTTGGCATGG 60.468 52.381 0.00 0.00 39.11 3.66
14 15 1.467883 CCGCATGTAAGTGTTGGCATG 60.468 52.381 0.00 0.00 40.96 4.06
15 16 0.810648 CCGCATGTAAGTGTTGGCAT 59.189 50.000 0.00 0.00 0.00 4.40
16 17 1.240641 CCCGCATGTAAGTGTTGGCA 61.241 55.000 0.00 0.00 0.00 4.92
17 18 1.506262 CCCGCATGTAAGTGTTGGC 59.494 57.895 0.00 0.00 0.00 4.52
18 19 1.506262 GCCCGCATGTAAGTGTTGG 59.494 57.895 0.00 0.00 0.00 3.77
19 20 1.240641 TGGCCCGCATGTAAGTGTTG 61.241 55.000 0.00 0.00 0.00 3.33
20 21 0.960364 CTGGCCCGCATGTAAGTGTT 60.960 55.000 0.00 0.00 0.00 3.32
21 22 1.377202 CTGGCCCGCATGTAAGTGT 60.377 57.895 0.00 0.00 0.00 3.55
22 23 2.114670 CCTGGCCCGCATGTAAGTG 61.115 63.158 0.00 0.00 0.00 3.16
23 24 2.272146 CCTGGCCCGCATGTAAGT 59.728 61.111 0.00 0.00 0.00 2.24
24 25 3.211963 GCCTGGCCCGCATGTAAG 61.212 66.667 7.66 0.00 0.00 2.34
25 26 4.813235 GGCCTGGCCCGCATGTAA 62.813 66.667 27.77 0.00 44.06 2.41
35 36 2.182842 CGCTTATGACAGGCCTGGC 61.183 63.158 35.42 34.37 39.62 4.85
36 37 2.182842 GCGCTTATGACAGGCCTGG 61.183 63.158 35.42 18.09 34.19 4.45
37 38 2.528743 CGCGCTTATGACAGGCCTG 61.529 63.158 31.60 31.60 0.00 4.85
38 39 2.202932 CGCGCTTATGACAGGCCT 60.203 61.111 5.56 0.00 0.00 5.19
39 40 1.644786 AAACGCGCTTATGACAGGCC 61.645 55.000 5.73 0.00 0.00 5.19
40 41 1.003851 TAAACGCGCTTATGACAGGC 58.996 50.000 5.73 0.00 0.00 4.85
41 42 3.733024 TTTAAACGCGCTTATGACAGG 57.267 42.857 5.73 0.00 0.00 4.00
42 43 5.320723 TCATTTTAAACGCGCTTATGACAG 58.679 37.500 5.73 0.00 0.00 3.51
43 44 5.284428 TCATTTTAAACGCGCTTATGACA 57.716 34.783 5.73 0.00 0.00 3.58
44 45 5.274641 CGTTCATTTTAAACGCGCTTATGAC 60.275 40.000 5.73 1.80 42.40 3.06
45 46 4.784045 CGTTCATTTTAAACGCGCTTATGA 59.216 37.500 5.73 3.87 42.40 2.15
46 47 4.784045 TCGTTCATTTTAAACGCGCTTATG 59.216 37.500 5.73 1.09 46.78 1.90
47 48 4.960329 TCGTTCATTTTAAACGCGCTTAT 58.040 34.783 5.73 0.00 46.78 1.73
48 49 4.386716 TCGTTCATTTTAAACGCGCTTA 57.613 36.364 5.73 0.41 46.78 3.09
49 50 3.256285 TCGTTCATTTTAAACGCGCTT 57.744 38.095 5.73 1.77 46.78 4.68
50 51 2.953640 TCGTTCATTTTAAACGCGCT 57.046 40.000 5.73 0.00 46.78 5.92
51 52 3.299446 CGATTCGTTCATTTTAAACGCGC 60.299 43.478 5.73 0.00 46.78 6.86
52 53 3.234284 CCGATTCGTTCATTTTAAACGCG 59.766 43.478 3.53 3.53 46.78 6.01
53 54 4.153256 ACCGATTCGTTCATTTTAAACGC 58.847 39.130 5.20 0.00 46.78 4.84
55 56 5.886480 CGACCGATTCGTTCATTTTAAAC 57.114 39.130 5.20 0.00 43.24 2.01
68 69 6.157211 ACCATGTCTATAAATCGACCGATTC 58.843 40.000 16.62 5.47 43.26 2.52
69 70 6.097915 ACCATGTCTATAAATCGACCGATT 57.902 37.500 11.39 11.39 45.67 3.34
70 71 5.723672 ACCATGTCTATAAATCGACCGAT 57.276 39.130 0.00 0.00 36.23 4.18
71 72 5.766670 ACTACCATGTCTATAAATCGACCGA 59.233 40.000 0.00 0.00 0.00 4.69
72 73 6.010294 ACTACCATGTCTATAAATCGACCG 57.990 41.667 0.00 0.00 0.00 4.79
73 74 8.658499 AAAACTACCATGTCTATAAATCGACC 57.342 34.615 0.00 0.00 0.00 4.79
82 83 9.816787 TTTTTCCCTAAAAACTACCATGTCTAT 57.183 29.630 0.00 0.00 39.16 1.98
83 84 9.816787 ATTTTTCCCTAAAAACTACCATGTCTA 57.183 29.630 0.00 0.00 44.95 2.59
84 85 8.721133 ATTTTTCCCTAAAAACTACCATGTCT 57.279 30.769 0.00 0.00 44.95 3.41
108 109 8.456471 GCCGAAAACTACCACTTTCTTATTAAT 58.544 33.333 0.00 0.00 30.80 1.40
109 110 7.444792 TGCCGAAAACTACCACTTTCTTATTAA 59.555 33.333 0.00 0.00 30.80 1.40
110 111 6.935771 TGCCGAAAACTACCACTTTCTTATTA 59.064 34.615 0.00 0.00 30.80 0.98
111 112 5.766174 TGCCGAAAACTACCACTTTCTTATT 59.234 36.000 0.00 0.00 30.80 1.40
112 113 5.310451 TGCCGAAAACTACCACTTTCTTAT 58.690 37.500 0.00 0.00 30.80 1.73
113 114 4.706035 TGCCGAAAACTACCACTTTCTTA 58.294 39.130 0.00 0.00 30.80 2.10
114 115 3.547746 TGCCGAAAACTACCACTTTCTT 58.452 40.909 0.00 0.00 30.80 2.52
115 116 3.202829 TGCCGAAAACTACCACTTTCT 57.797 42.857 0.00 0.00 30.80 2.52
116 117 5.616488 TTATGCCGAAAACTACCACTTTC 57.384 39.130 0.00 0.00 0.00 2.62
117 118 6.584185 ATTTATGCCGAAAACTACCACTTT 57.416 33.333 0.00 0.00 0.00 2.66
118 119 6.584185 AATTTATGCCGAAAACTACCACTT 57.416 33.333 0.00 0.00 0.00 3.16
119 120 6.015772 ACAAATTTATGCCGAAAACTACCACT 60.016 34.615 0.00 0.00 0.00 4.00
120 121 6.153756 ACAAATTTATGCCGAAAACTACCAC 58.846 36.000 0.00 0.00 0.00 4.16
121 122 6.334102 ACAAATTTATGCCGAAAACTACCA 57.666 33.333 0.00 0.00 0.00 3.25
122 123 8.745464 TTTACAAATTTATGCCGAAAACTACC 57.255 30.769 0.00 0.00 0.00 3.18
123 124 9.401873 ACTTTACAAATTTATGCCGAAAACTAC 57.598 29.630 0.00 0.00 0.00 2.73
124 125 9.400638 CACTTTACAAATTTATGCCGAAAACTA 57.599 29.630 0.00 0.00 0.00 2.24
125 126 7.383843 CCACTTTACAAATTTATGCCGAAAACT 59.616 33.333 0.00 0.00 0.00 2.66
126 127 7.170151 ACCACTTTACAAATTTATGCCGAAAAC 59.830 33.333 0.00 0.00 0.00 2.43
127 128 7.210873 ACCACTTTACAAATTTATGCCGAAAA 58.789 30.769 0.00 0.00 0.00 2.29
128 129 6.750148 ACCACTTTACAAATTTATGCCGAAA 58.250 32.000 0.00 0.00 0.00 3.46
129 130 6.334102 ACCACTTTACAAATTTATGCCGAA 57.666 33.333 0.00 0.00 0.00 4.30
130 131 5.968528 ACCACTTTACAAATTTATGCCGA 57.031 34.783 0.00 0.00 0.00 5.54
131 132 6.848451 ACTACCACTTTACAAATTTATGCCG 58.152 36.000 0.00 0.00 0.00 5.69
132 133 8.921670 CAAACTACCACTTTACAAATTTATGCC 58.078 33.333 0.00 0.00 0.00 4.40
133 134 9.471084 ACAAACTACCACTTTACAAATTTATGC 57.529 29.630 0.00 0.00 0.00 3.14
137 138 8.139350 GCCTACAAACTACCACTTTACAAATTT 58.861 33.333 0.00 0.00 0.00 1.82
138 139 7.285858 TGCCTACAAACTACCACTTTACAAATT 59.714 33.333 0.00 0.00 0.00 1.82
139 140 6.773685 TGCCTACAAACTACCACTTTACAAAT 59.226 34.615 0.00 0.00 0.00 2.32
140 141 6.038492 GTGCCTACAAACTACCACTTTACAAA 59.962 38.462 0.00 0.00 0.00 2.83
141 142 5.528320 GTGCCTACAAACTACCACTTTACAA 59.472 40.000 0.00 0.00 0.00 2.41
142 143 5.058490 GTGCCTACAAACTACCACTTTACA 58.942 41.667 0.00 0.00 0.00 2.41
143 144 4.151157 CGTGCCTACAAACTACCACTTTAC 59.849 45.833 0.00 0.00 0.00 2.01
144 145 4.309099 CGTGCCTACAAACTACCACTTTA 58.691 43.478 0.00 0.00 0.00 1.85
145 146 3.135994 CGTGCCTACAAACTACCACTTT 58.864 45.455 0.00 0.00 0.00 2.66
146 147 2.549349 CCGTGCCTACAAACTACCACTT 60.549 50.000 0.00 0.00 0.00 3.16
147 148 1.001633 CCGTGCCTACAAACTACCACT 59.998 52.381 0.00 0.00 0.00 4.00
148 149 1.270465 ACCGTGCCTACAAACTACCAC 60.270 52.381 0.00 0.00 0.00 4.16
149 150 1.050204 ACCGTGCCTACAAACTACCA 58.950 50.000 0.00 0.00 0.00 3.25
150 151 2.174363 AACCGTGCCTACAAACTACC 57.826 50.000 0.00 0.00 0.00 3.18
151 152 4.511082 TGTTAAACCGTGCCTACAAACTAC 59.489 41.667 0.00 0.00 0.00 2.73
152 153 4.701765 TGTTAAACCGTGCCTACAAACTA 58.298 39.130 0.00 0.00 0.00 2.24
153 154 3.543665 TGTTAAACCGTGCCTACAAACT 58.456 40.909 0.00 0.00 0.00 2.66
154 155 3.967203 TGTTAAACCGTGCCTACAAAC 57.033 42.857 0.00 0.00 0.00 2.93
155 156 4.978083 TTTGTTAAACCGTGCCTACAAA 57.022 36.364 0.00 0.00 34.28 2.83
156 157 4.261656 CCATTTGTTAAACCGTGCCTACAA 60.262 41.667 0.00 0.00 0.00 2.41
157 158 3.253677 CCATTTGTTAAACCGTGCCTACA 59.746 43.478 0.00 0.00 0.00 2.74
158 159 3.253921 ACCATTTGTTAAACCGTGCCTAC 59.746 43.478 0.00 0.00 0.00 3.18
159 160 3.253677 CACCATTTGTTAAACCGTGCCTA 59.746 43.478 0.00 0.00 0.00 3.93
160 161 2.035321 CACCATTTGTTAAACCGTGCCT 59.965 45.455 0.00 0.00 0.00 4.75
161 162 2.399448 CACCATTTGTTAAACCGTGCC 58.601 47.619 0.00 0.00 0.00 5.01
162 163 2.223852 ACCACCATTTGTTAAACCGTGC 60.224 45.455 0.00 0.00 0.00 5.34
163 164 3.719173 ACCACCATTTGTTAAACCGTG 57.281 42.857 0.00 0.00 0.00 4.94
164 165 4.463070 ACTACCACCATTTGTTAAACCGT 58.537 39.130 0.00 0.00 0.00 4.83
165 166 5.441709 AACTACCACCATTTGTTAAACCG 57.558 39.130 0.00 0.00 0.00 4.44
194 195 9.434275 TGATGATCCCTTAACTGAGAGTATTTA 57.566 33.333 0.00 0.00 0.00 1.40
195 196 8.324191 TGATGATCCCTTAACTGAGAGTATTT 57.676 34.615 0.00 0.00 0.00 1.40
196 197 7.921041 TGATGATCCCTTAACTGAGAGTATT 57.079 36.000 0.00 0.00 0.00 1.89
197 198 7.921041 TTGATGATCCCTTAACTGAGAGTAT 57.079 36.000 0.00 0.00 0.00 2.12
198 199 7.147655 CCTTTGATGATCCCTTAACTGAGAGTA 60.148 40.741 0.00 0.00 0.00 2.59
199 200 6.352565 CCTTTGATGATCCCTTAACTGAGAGT 60.353 42.308 0.00 0.00 0.00 3.24
200 201 6.054295 CCTTTGATGATCCCTTAACTGAGAG 58.946 44.000 0.00 0.00 0.00 3.20
201 202 5.104360 CCCTTTGATGATCCCTTAACTGAGA 60.104 44.000 0.00 0.00 0.00 3.27
205 206 3.269381 TGCCCTTTGATGATCCCTTAACT 59.731 43.478 0.00 0.00 0.00 2.24
208 209 2.423373 GCTGCCCTTTGATGATCCCTTA 60.423 50.000 0.00 0.00 0.00 2.69
229 230 1.597461 GTTGACCCTCCTTCCCTCG 59.403 63.158 0.00 0.00 0.00 4.63
235 236 1.765597 GACCACGGTTGACCCTCCTT 61.766 60.000 0.00 0.00 0.00 3.36
248 249 5.569413 GTTGCCAATTCTATTTAGACCACG 58.431 41.667 0.00 0.00 30.81 4.94
323 334 0.537188 ATGAATCCTCACCTTCGCGT 59.463 50.000 5.77 0.00 33.30 6.01
331 342 2.420022 CCAACGTCCAATGAATCCTCAC 59.580 50.000 0.00 0.00 33.30 3.51
335 346 1.743394 GGTCCAACGTCCAATGAATCC 59.257 52.381 0.00 0.00 0.00 3.01
380 393 2.063015 ATGTGAACTTGGACCCGGCA 62.063 55.000 0.00 0.00 0.00 5.69
381 394 1.303317 ATGTGAACTTGGACCCGGC 60.303 57.895 0.00 0.00 0.00 6.13
382 395 0.250727 ACATGTGAACTTGGACCCGG 60.251 55.000 0.00 0.00 0.00 5.73
383 396 1.156736 GACATGTGAACTTGGACCCG 58.843 55.000 1.15 0.00 0.00 5.28
384 397 2.154462 CAGACATGTGAACTTGGACCC 58.846 52.381 1.15 0.00 0.00 4.46
385 398 2.154462 CCAGACATGTGAACTTGGACC 58.846 52.381 1.15 0.00 0.00 4.46
386 399 1.537202 GCCAGACATGTGAACTTGGAC 59.463 52.381 1.15 0.00 0.00 4.02
387 400 1.545428 GGCCAGACATGTGAACTTGGA 60.545 52.381 1.15 0.00 0.00 3.53
496 532 0.469892 AGGGGGTTTGTTGCTTCCAG 60.470 55.000 0.00 0.00 0.00 3.86
497 533 0.469144 GAGGGGGTTTGTTGCTTCCA 60.469 55.000 0.00 0.00 0.00 3.53
498 534 1.185618 GGAGGGGGTTTGTTGCTTCC 61.186 60.000 0.00 0.00 0.00 3.46
548 587 1.268283 GGGAGTGGTGGAGGAAGAGG 61.268 65.000 0.00 0.00 0.00 3.69
549 588 0.545309 TGGGAGTGGTGGAGGAAGAG 60.545 60.000 0.00 0.00 0.00 2.85
550 589 0.104672 TTGGGAGTGGTGGAGGAAGA 60.105 55.000 0.00 0.00 0.00 2.87
551 590 0.036875 GTTGGGAGTGGTGGAGGAAG 59.963 60.000 0.00 0.00 0.00 3.46
552 591 1.423794 GGTTGGGAGTGGTGGAGGAA 61.424 60.000 0.00 0.00 0.00 3.36
664 703 1.690219 CCAGGTGGCTAGGTGGCTAG 61.690 65.000 0.00 0.00 42.34 3.42
665 704 1.689233 CCAGGTGGCTAGGTGGCTA 60.689 63.158 0.00 0.00 42.34 3.93
779 827 3.770040 CTGGATCGCACCGTGGGA 61.770 66.667 19.42 19.42 43.55 4.37
910 972 0.678395 CTGCTGCTCGTATGGGATCT 59.322 55.000 0.00 0.00 0.00 2.75
911 973 0.948141 GCTGCTGCTCGTATGGGATC 60.948 60.000 8.53 0.00 36.03 3.36
918 980 2.125793 CTGCTGCTGCTGCTCGTA 60.126 61.111 27.67 10.41 40.48 3.43
969 1043 2.046023 TGGCTGCCACGAGGATTG 60.046 61.111 19.30 0.00 36.89 2.67
970 1044 2.249413 CTCTGGCTGCCACGAGGATT 62.249 60.000 26.83 0.00 36.89 3.01
972 1046 3.385384 CTCTGGCTGCCACGAGGA 61.385 66.667 26.83 18.99 36.89 3.71
981 1055 3.054503 GTGTGCTGGCTCTGGCTG 61.055 66.667 0.00 0.00 38.73 4.85
982 1056 2.421923 ATTGTGTGCTGGCTCTGGCT 62.422 55.000 0.00 0.00 38.73 4.75
983 1057 1.975407 ATTGTGTGCTGGCTCTGGC 60.975 57.895 0.00 0.00 37.82 4.85
984 1058 1.592400 CCATTGTGTGCTGGCTCTGG 61.592 60.000 0.00 0.00 0.00 3.86
985 1059 1.880894 CCATTGTGTGCTGGCTCTG 59.119 57.895 0.00 0.00 0.00 3.35
986 1060 4.410225 CCATTGTGTGCTGGCTCT 57.590 55.556 0.00 0.00 0.00 4.09
990 1064 1.642037 CTCTCGCCATTGTGTGCTGG 61.642 60.000 0.00 0.00 35.53 4.85
991 1065 1.642037 CCTCTCGCCATTGTGTGCTG 61.642 60.000 0.00 0.00 0.00 4.41
1629 1723 4.774503 AGGAAGCCGCAGAGCAGC 62.775 66.667 0.00 0.00 34.23 5.25
2277 2371 4.778143 ACAATGTCCGCGAGCCCC 62.778 66.667 8.23 0.00 0.00 5.80
2357 2451 0.375454 CACAGACAAAACGAACGCCA 59.625 50.000 0.00 0.00 0.00 5.69
2404 2498 0.527817 GATCGGGCAAGTCCTACACG 60.528 60.000 0.00 0.00 34.39 4.49
2478 2572 3.842820 CCATATCACTCTAGTCATGGCG 58.157 50.000 0.00 0.00 0.00 5.69
2494 2592 1.805120 GCACGTTACACCGAGCCATAT 60.805 52.381 0.00 0.00 38.28 1.78
2550 2650 0.169009 GGCACAAATCCTCGCAAGTC 59.831 55.000 0.00 0.00 39.48 3.01
2636 2744 2.158842 CCCTTCCTATCACAAGGAGCAG 60.159 54.545 0.00 0.00 46.29 4.24
2639 2747 4.021894 CGTATCCCTTCCTATCACAAGGAG 60.022 50.000 0.00 0.00 46.29 3.69
2643 2751 5.278808 CGAATCGTATCCCTTCCTATCACAA 60.279 44.000 0.00 0.00 0.00 3.33
2646 2754 4.659115 TCGAATCGTATCCCTTCCTATCA 58.341 43.478 1.52 0.00 0.00 2.15
2650 2758 3.497332 TCATCGAATCGTATCCCTTCCT 58.503 45.455 1.52 0.00 0.00 3.36
2651 2759 3.936372 TCATCGAATCGTATCCCTTCC 57.064 47.619 1.52 0.00 0.00 3.46
2652 2760 4.859798 GTGATCATCGAATCGTATCCCTTC 59.140 45.833 1.52 0.00 0.00 3.46
2653 2761 4.280929 TGTGATCATCGAATCGTATCCCTT 59.719 41.667 1.52 0.00 0.00 3.95
2654 2762 3.826729 TGTGATCATCGAATCGTATCCCT 59.173 43.478 1.52 0.00 0.00 4.20
2655 2763 4.174411 TGTGATCATCGAATCGTATCCC 57.826 45.455 1.52 0.00 0.00 3.85
2656 2764 4.564372 CCATGTGATCATCGAATCGTATCC 59.436 45.833 1.52 1.16 31.15 2.59
2721 2841 2.742053 GCACGATTCCTAGCAGTTCAAA 59.258 45.455 0.00 0.00 0.00 2.69
2722 2842 2.028112 AGCACGATTCCTAGCAGTTCAA 60.028 45.455 0.00 0.00 0.00 2.69
2759 2879 9.213777 ACAGATAGATTCCACTTATAACAGGAA 57.786 33.333 13.49 13.49 43.63 3.36
2761 2881 8.642432 TCACAGATAGATTCCACTTATAACAGG 58.358 37.037 0.00 0.00 0.00 4.00
2776 2896 6.072175 GGTAAGCTCGAGAATCACAGATAGAT 60.072 42.308 18.75 0.00 33.17 1.98
2778 2898 5.240623 AGGTAAGCTCGAGAATCACAGATAG 59.759 44.000 18.75 0.00 33.17 2.08
2779 2899 5.133941 AGGTAAGCTCGAGAATCACAGATA 58.866 41.667 18.75 0.00 33.17 1.98
2784 2904 3.701241 CTGAGGTAAGCTCGAGAATCAC 58.299 50.000 18.75 7.45 33.17 3.06
2790 2910 0.749649 ATGGCTGAGGTAAGCTCGAG 59.250 55.000 8.45 8.45 43.06 4.04
2815 4983 4.010349 CAGGGTCTAATCCTTTTGACACC 58.990 47.826 0.00 0.00 40.52 4.16
2832 5000 2.422377 GGTGTGTTAGACCAAACAGGGT 60.422 50.000 0.00 0.00 46.02 4.34
2834 5002 2.878406 CAGGTGTGTTAGACCAAACAGG 59.122 50.000 0.00 0.00 39.92 4.00
2835 5003 3.541632 ACAGGTGTGTTAGACCAAACAG 58.458 45.455 0.00 0.00 39.92 3.16
2845 5013 6.097270 AGAGGCGTATATTAACAGGTGTGTTA 59.903 38.462 0.00 0.00 45.48 2.41
2848 5016 4.745125 CAGAGGCGTATATTAACAGGTGTG 59.255 45.833 0.00 0.00 0.00 3.82
2849 5017 4.739735 GCAGAGGCGTATATTAACAGGTGT 60.740 45.833 0.00 0.00 0.00 4.16
2850 5018 3.741344 GCAGAGGCGTATATTAACAGGTG 59.259 47.826 0.00 0.00 0.00 4.00
2853 5021 3.990469 CCTGCAGAGGCGTATATTAACAG 59.010 47.826 17.39 0.00 45.35 3.16
2855 5023 3.988517 GACCTGCAGAGGCGTATATTAAC 59.011 47.826 17.39 0.00 44.33 2.01
2857 5025 2.228103 CGACCTGCAGAGGCGTATATTA 59.772 50.000 17.39 0.00 44.33 0.98
2858 5026 1.000163 CGACCTGCAGAGGCGTATATT 60.000 52.381 17.39 0.00 44.33 1.28
2859 5027 0.598562 CGACCTGCAGAGGCGTATAT 59.401 55.000 17.39 0.00 44.33 0.86
2860 5028 1.452953 CCGACCTGCAGAGGCGTATA 61.453 60.000 23.22 0.00 44.33 1.47
2862 5030 3.449227 CCGACCTGCAGAGGCGTA 61.449 66.667 23.22 0.00 44.33 4.42
2864 5032 3.883744 AAACCGACCTGCAGAGGCG 62.884 63.158 17.39 18.87 44.33 5.52
2865 5033 2.032681 AAACCGACCTGCAGAGGC 59.967 61.111 17.39 6.63 44.33 4.70
2867 5035 1.813513 AATGAAACCGACCTGCAGAG 58.186 50.000 17.39 8.04 0.00 3.35
2869 5037 2.665519 CGAAAATGAAACCGACCTGCAG 60.666 50.000 6.78 6.78 0.00 4.41
2870 5038 1.265635 CGAAAATGAAACCGACCTGCA 59.734 47.619 0.00 0.00 0.00 4.41
2871 5039 1.401018 CCGAAAATGAAACCGACCTGC 60.401 52.381 0.00 0.00 0.00 4.85
2872 5040 1.401018 GCCGAAAATGAAACCGACCTG 60.401 52.381 0.00 0.00 0.00 4.00
2873 5041 0.879090 GCCGAAAATGAAACCGACCT 59.121 50.000 0.00 0.00 0.00 3.85
2874 5042 0.109458 GGCCGAAAATGAAACCGACC 60.109 55.000 0.00 0.00 0.00 4.79
2875 5043 0.109458 GGGCCGAAAATGAAACCGAC 60.109 55.000 0.00 0.00 0.00 4.79
2889 5057 2.016961 CATGAGTGATTTCGGGCCG 58.983 57.895 22.51 22.51 0.00 6.13
2891 5059 1.728490 GGGCATGAGTGATTTCGGGC 61.728 60.000 0.00 0.00 0.00 6.13
2893 5061 1.019673 CTGGGCATGAGTGATTTCGG 58.980 55.000 0.00 0.00 0.00 4.30
2894 5062 1.742761 ACTGGGCATGAGTGATTTCG 58.257 50.000 0.00 0.00 0.00 3.46
2895 5063 4.517285 TCTTACTGGGCATGAGTGATTTC 58.483 43.478 0.00 0.00 0.00 2.17
2896 5064 4.574674 TCTTACTGGGCATGAGTGATTT 57.425 40.909 0.00 0.00 0.00 2.17
2898 5066 4.655649 TGTATCTTACTGGGCATGAGTGAT 59.344 41.667 0.00 0.00 0.00 3.06
2899 5067 4.030216 TGTATCTTACTGGGCATGAGTGA 58.970 43.478 0.00 0.00 0.00 3.41
2902 5070 4.679373 AGTGTATCTTACTGGGCATGAG 57.321 45.455 0.00 0.00 0.00 2.90
2903 5071 4.225042 ACAAGTGTATCTTACTGGGCATGA 59.775 41.667 0.00 0.00 34.66 3.07
2904 5072 4.517285 ACAAGTGTATCTTACTGGGCATG 58.483 43.478 0.00 0.00 34.66 4.06
2906 5074 5.748670 TTACAAGTGTATCTTACTGGGCA 57.251 39.130 0.00 0.00 34.66 5.36
2907 5075 7.625828 AATTTACAAGTGTATCTTACTGGGC 57.374 36.000 0.00 0.00 34.66 5.36
2937 5105 9.650539 TGGATTTGATGTAATTTAACACAATGG 57.349 29.630 0.00 0.00 30.75 3.16
2942 5110 7.540745 ACGCTTGGATTTGATGTAATTTAACAC 59.459 33.333 0.00 0.00 30.75 3.32
2962 5130 0.734889 CATTCCTAAGGCCACGCTTG 59.265 55.000 5.01 0.00 0.00 4.01
2963 5131 0.618458 TCATTCCTAAGGCCACGCTT 59.382 50.000 5.01 0.00 0.00 4.68
2964 5132 0.179000 CTCATTCCTAAGGCCACGCT 59.821 55.000 5.01 0.00 0.00 5.07
2965 5133 0.107654 ACTCATTCCTAAGGCCACGC 60.108 55.000 5.01 0.00 0.00 5.34
2966 5134 2.693591 TCTACTCATTCCTAAGGCCACG 59.306 50.000 5.01 0.00 0.00 4.94
2967 5135 4.698575 CTTCTACTCATTCCTAAGGCCAC 58.301 47.826 5.01 0.00 0.00 5.01
2968 5136 3.134804 GCTTCTACTCATTCCTAAGGCCA 59.865 47.826 5.01 0.00 0.00 5.36
2969 5137 3.389656 AGCTTCTACTCATTCCTAAGGCC 59.610 47.826 0.00 0.00 0.00 5.19
2970 5138 4.100189 TCAGCTTCTACTCATTCCTAAGGC 59.900 45.833 0.00 0.00 0.00 4.35
2972 5140 6.463995 ACTCAGCTTCTACTCATTCCTAAG 57.536 41.667 0.00 0.00 0.00 2.18
2975 5143 4.647399 GGTACTCAGCTTCTACTCATTCCT 59.353 45.833 0.00 0.00 0.00 3.36
2976 5144 4.647399 AGGTACTCAGCTTCTACTCATTCC 59.353 45.833 0.00 0.00 0.00 3.01
2978 5146 6.613153 AAAGGTACTCAGCTTCTACTCATT 57.387 37.500 0.00 0.00 41.59 2.57
2979 5147 6.183360 CGTAAAGGTACTCAGCTTCTACTCAT 60.183 42.308 0.00 0.00 41.59 2.90
2981 5149 5.353678 TCGTAAAGGTACTCAGCTTCTACTC 59.646 44.000 0.00 0.00 41.59 2.59
2982 5150 5.251764 TCGTAAAGGTACTCAGCTTCTACT 58.748 41.667 0.00 0.00 41.59 2.57
2983 5151 5.557891 TCGTAAAGGTACTCAGCTTCTAC 57.442 43.478 0.00 0.00 41.59 2.59
2985 5153 4.523558 ACTTCGTAAAGGTACTCAGCTTCT 59.476 41.667 0.00 0.00 41.59 2.85
2986 5154 4.807443 ACTTCGTAAAGGTACTCAGCTTC 58.193 43.478 0.00 0.00 41.59 3.86
2987 5155 4.868314 ACTTCGTAAAGGTACTCAGCTT 57.132 40.909 0.00 0.00 44.28 3.74
2989 5157 5.100943 CCTAACTTCGTAAAGGTACTCAGC 58.899 45.833 0.00 0.00 38.49 4.26
2990 5158 6.506500 TCCTAACTTCGTAAAGGTACTCAG 57.493 41.667 0.00 0.00 38.49 3.35
2991 5159 6.265196 TGTTCCTAACTTCGTAAAGGTACTCA 59.735 38.462 0.00 0.00 38.49 3.41
2994 5162 5.635280 GGTGTTCCTAACTTCGTAAAGGTAC 59.365 44.000 0.00 0.00 36.78 3.34
2995 5163 5.564651 CGGTGTTCCTAACTTCGTAAAGGTA 60.565 44.000 0.00 0.00 36.78 3.08
2997 5165 3.676646 CGGTGTTCCTAACTTCGTAAAGG 59.323 47.826 0.00 0.00 36.78 3.11
2998 5166 4.301628 ACGGTGTTCCTAACTTCGTAAAG 58.698 43.478 8.40 0.00 38.30 1.85
2999 5167 4.320608 ACGGTGTTCCTAACTTCGTAAA 57.679 40.909 8.40 0.00 38.30 2.01
3012 5209 5.059161 AGGGTTTTAAAGTCTACGGTGTTC 58.941 41.667 0.00 0.00 0.00 3.18
3014 5211 4.694760 AGGGTTTTAAAGTCTACGGTGT 57.305 40.909 0.00 0.00 0.00 4.16
3015 5212 5.787380 ACTAGGGTTTTAAAGTCTACGGTG 58.213 41.667 0.00 0.00 0.00 4.94
3017 5214 7.163001 ACTACTAGGGTTTTAAAGTCTACGG 57.837 40.000 0.00 0.00 0.00 4.02
3183 5615 3.453988 CCCGTGTTTGTTGGGCAT 58.546 55.556 0.00 0.00 35.82 4.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.